Sequence
atgc intronic sequence ATGC exonic sequence...tgtgaactttcttgagtatcaatgggattcctcaagtatacaatgacttccatgttatatcttttattctttaatcccttggcatcctctgttctttcagGCAAGGATGTCCTAGCTAAGGCCAAAACAGGAACTGGGAAAACTGTAGCGTTTTTG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G63630.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G63630.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G026371_T02 (Zea mays), 3'ss of exon 2
tgtgaactttcttgagtatcaatgggattcctcaagtatacaatgacttccatgttatatcttttattctttaatcccttggcatcctctgttctttcagGCAAGGATGTCCTAGCTAAGGCCAAAACAGGAACTGGGAAAACTGTAGCGTTTTTG
| | || | ||| || | || || | || || || | | | | | || | | | | |||||||||||| || || ||||| || ||||||||||||||||| || || ||||||
-----gtcggtgaaaatgcaaaagctattgcttagcattataa--aattaaatcttgggaggtcttgaaggtgacatttcaatattttgttgccatgtagGCAAGGATGTTCTTGCAAAGGCAAAGACAGGAACTGGGAAAACAGTTGCCTTTTTG
upper sequence: AT5G63630.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA07G06240.1 (Glycine max), 3'ss of exon 2
tgtgaactttcttgagtatcaatgggattcc--tcaagtatacaatgacttccatgttatatcttttattctttaatcccttggcatcctctgttctttcagGCAAGGATGTCCTAGCTAAGGCCAAAACAGGAACTGGGAAAACTGTAGCGTTTTTG
| ||| | | | | | | | | | | | | || | ||||||| | | ||| | | ||||||| ||||||||||| || |||||||| ||||| || || ||||| ||||| ||||||
--taaacaggaaagcaatttattccagctttggttgacattgttctcatatatgtcttgagttttttattatggtgactcttattccaattaatattttcagGTAAGGATGTCCTTGCCAAGGCCAAGACAGGCACCGGAAAAACAGTAGCCTTTTTG
upper sequence: AT5G63630.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv15s0046g01010.t01 (Vitis vinifera), 3'ss of exon 3
----tgtgaactttcttgagtatcaatgggattcctcaagtatacaatgacttccatgttatatcttttattctttaatcccttggcatcctctgttctttcagGCAAGGATGTCCTAGCTAAGGCCAAAACAGGAACTGGGAAAACTGTAGCGTTTTTG
| | || || || | || | | ||||| | ||| || | || | | | | ||| | |||| || ||| |||||||| ||||| || || |||||||| |||||||||||||| || ||||||
ctattttaccgttgtttatgttcccatttattctatttagtatg---tttctttaattctcagatttctgtggggct-tactctggtgagttgtgtttttatagGTAAGGATGTTCTAGCCAAAGCTAAAACAGGCACTGGGAAAACTGTCGCATTTTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acttccatgttatatcttttattctttaatcccttggcatcctctgttctttcagGCAAGGATGTCCTAGCTAAGGCCAAAACAGGAACTGGGAAAACTGTAGCGTTTTTG
ctttaat putative branch site (score: 4)
catcctctgttctttc putative PPT
atgttatatcttttat TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtgaactttcttgagtatcaatgggattcctcaagtatacaatgacttccatgttatatcttttattctttaatcccttggcatcctctgttctttcagGCAAGGATGTCCTAGCTAAGGCCAAAACAGGAACTGGGAAAACTGTAGCGTTTTTG
- - - - - - - - - - - - - - tcctcaa
- - - - - - - - - - - - - - - - - - - -acaatga